Related papers: Solution decomposition for the nonlinear Poisson-B…
The classical problem of two uniformly charged infinite planes in electrochemical equilibrium with an infinite monovalent salt reservoir is solved exactly at the mean-field nonlinear Poisson-Boltzmann (PB) level, including an explicit…
We develop an efficient and reliable adaptive finite element method (AFEM) for the nonlinear Poisson-Boltzmann equation (PBE). We first examine the regularization technique of Chen, Holst, and Xu; this technique made possible the first a…
The Poisson-Boltzmann equation offers an efficient way to study electrostatics in molecular settings. Its numerical solution with the boundary element method is widely used, as the complicated molecular surface is accurately represented by…
In this paper, we solve the linearized Poisson-Boltzmann equation, used to model the electric potential of macromolecules in a solvent. We derive a corrected trapezoidal rule with improved accuracy for a boundary integral formulation of the…
The Poisson--Boltzmann equation is widely used to model electrostatics in molecular systems. Available software packages solve it using finite difference, finite element, and boundary element methods, where the latter is attractive due to…
The description of a conducting medium in thermal equilibrium, such as an electrolyte solution or a plasma, involves nonlinear electrostatics, a subject rarely discussed in the standard electricity and magnetism textbooks. We consider in…
The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into…
The size-modified Poisson-Boltzmann equation (SMPBE) is one important variant of the popular dielectric model, the Poisson-Boltzmann equation (PBE), to reflect ionic size effects in the prediction of electrostatics for a biomolecule in an…
A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…
In this paper, we present an analytical solution to nonlocal continuum electrostatics for an arbitrary charge distribution in a spherical solute. Our approach relies on two key steps: (1) re-formulating the PDE problem using…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
A variational approach is used to develop a robust numerical procedure for solving the nonlinear Poisson-Boltzmann equation. Following Maggs et al., we construct an appropriate constrained free energy functional, such that its…
The Poisson-Boltzmann equation is a nonlinear elliptic equation with Dirac distribution sources, which has been widely applied to the prediction of electrostatics potential of biological biomolecular systems in solution. In this paper, we…
In this paper, we develop a domain decomposition method for the nonlinear Poisson-Boltzmann equation based on a solvent-excluded surface widely used in computational chemistry. The model relies on a nonlinear equation defined in…
We consider the Poisson-Boltzmann equation in a periodic cell, representative of a porous medium. It is a model for the electrostatic distribution of $N$ chemical species diluted in a liquid at rest, occupying the pore space with charged…
Poisson-Boltzmann (PB) theory is the classic approach to soft matter electrostatics which has been applied to numerous problems of physical chemistry and biophysics. Its essential limitations are the neglect of correlation effects and of…
A finite element discretization using a method of lines approached is proposed for approximately solving the Poisson-Nernst-Planck (PNP) equations. This discretization scheme enforces positivity of the computed solutions, corresponding to…
Efficient and stable solution of partial differential equations (PDEs) is central to scientific and engineering applications, yet existing numerical solvers rely heavily on matrix based discretizations, while learning based methods require…
The Poisson-Boltzmann (PB) equation provides a mean-field theory of electrolyte solutions at interfaces and in confinement, describing how ions reorganize close to charged surfaces to form the so-called electrical double layer (EDL), with…
We present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the…